Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

These are the micro-array results of a differential gene expression microarray experiments and the subsequent analysis steps performed on them. The up/down- regulation ratio was obtained by measuring WT cells against MK5 activated cells. See material and methods for technical information as well as the data usage policy.

MK5 Proteome Analysis

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.


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Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 213 to 262 of 16578 in total
Value Type  : Ranked
Filtered  : 1
Rank
description
Network Comparison Type
Interaction Map
red
green
network_comparison
54 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] Subtracted High confidence 185.678 245.247 59.569
brachyury protein (t protein). [swissprot;acc:o15178] Low confidence 224.922 202.592 22.33
cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] Divided 267.448 240.822 1.11056
transcription factor jun-d. [swissprot;acc:p17535] High confidence 200.941 158.941 1.26425
55 cysteine-rich protein 1 (cysteine-rich intestinal protein) (crip) (cysteine-rich heart protein) (hcrhp). [swissprot;acc:p50238] Subtracted Low confidence 230.944 209.149 21.795
cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627] Divided 267.376 240.78 1.11046
glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] Subtracted High confidence 185.678 245.247 59.569
protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690] Divided 320.927 254.434 1.26134
56 brachyury protein (t protein). [swissprot;acc:o15178] Low confidence 224.922 202.592 1.11022
glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] Subtracted High confidence 185.678 245.247 59.569
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262] Divided 266.856 336.233 1.25998
set and mynd domain containing 2; hskm-b protein; zinc finger, mynd domain containing 14. [refseq;acc:nm_020197] Subtracted Low confidence 230.944 209.149 21.795
57 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6] Divided High confidence 266.856 336.233 1.25998
myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] Subtracted 185.678 245.247 59.569
proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100] Divided Low confidence 202.802 182.73 1.10985
set and mynd domain containing protein 1. [sptrembl;acc:q8nb12] Subtracted 230.944 209.149 21.795
58 glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] High confidence 185.678 245.247 59.569
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150] Divided 266.863 336.191 1.25979
jun dimerization protein. [refseq;acc:nm_130469] Low confidence 202.802 182.73 1.10985
putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] Subtracted 155.56 133.876 21.684
59 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798] Divided High confidence 266.863 336.19 1.25978
mitochondrial tumor suppressor gene 1; transcription factor mtsg1; at2 receptor-interacting protein 1; erythroid differentiation-related gene. [refseq;acc:nm_020749] Subtracted Low confidence 221.902 200.783 21.119
nadh-ubiquinone oxidoreductase subunit b17.2 (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b17.2) (ci-b17.2) (cib17.2) (13 kda differentiation-associated protein). [swissprot;acc:q9ui09] Divided 233.134 210.267 1.10875
potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] Subtracted High confidence 269.278 327.709 58.431
60 cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929] 269.254 327.655 58.401
fos-related antigen 2. [swissprot;acc:p15408] Divided Low confidence 202.793 182.961 1.10839
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08] High confidence 266.864 336.184 1.25976
malignant cell expression-enhanced gene/tumor progression-enhanc. [refseq;acc:nm_024298] Subtracted Low confidence 211 231.635 20.635
61 amyloid beta a4 precursor protein-binding family a member 1 (neuron- specific x11 protein) (neuronal munc18-1-interacting protein 1) (mint-1) (adapter protein x11alpha). [swissprot;acc:q02410] 229.144 208.803 20.341
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670] Divided High confidence 266.864 336.182 1.25975
potassium voltage-gated channel, shal-related subfamily, member 3 isoform 1; sha1-related potassium channel kv4.3; voltage-gated k+ channel; potassium ionic channel kv4.3; voltage-gated potassium channel kv4.3. [refseq;acc:nm_004980] Subtracted 269.248 327.642 58.394
protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] Divided Low confidence 202.792 182.974 1.10831
62 fos-related antigen 1 (fra-1). [swissprot;acc:p15407] 202.79 183.017 1.10804
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151] High confidence 266.865 336.181 1.25974
potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979] Subtracted 269.23 327.601 58.371
proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100] Low confidence 202.802 182.73 20.072
63 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] Divided High confidence 266.865 336.178 1.25973
jun dimerization protein. [refseq;acc:nm_130469] Subtracted Low confidence 202.802 182.73 20.072
nuclear transcription factor y subunit gamma (nf-y protein chain c) (nuclear factor yc) (nf-yc) (ccaat-binding transcription factor subunit c) (cbf-c) (transactivator hsm-1/2). [swissprot;acc:q13952] High confidence 260.532 204.309 56.223
putative rna-binding protein 7 (rna binding motif protein 7). [swissprot;acc:q9y580] Divided Low confidence 265.688 239.902 1.10749
64 ccaat-binding transcription factor subunit b (cbf-b) (nf-y protein chain a) (nf-ya) (caat-box dna binding protein subunit a). [swissprot;acc:p23511] Subtracted High confidence 260.532 204.309 56.223
fos-related antigen 2. [swissprot;acc:p15408] Low confidence 202.793 182.961 19.832
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] Divided High confidence 266.868 336.159 1.25965
transcription factor jun-d. [swissprot;acc:p17535] Low confidence 202.709 183.361 1.10552
65 guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148] High confidence 267.136 336.077 1.25807
protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] Subtracted Low confidence 202.792 182.974 19.818
serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, alpha isoform (pp2a, subunit b, b-alpha isoform) (pp2a, subunit b, b55-alpha isoform) (pp2a, subunit b, pr55-alpha isoform) (pp2a, subunit b, r2-alpha isoform). [swissprot;acc:q00007] High confidence 187.457 243.678 56.221
transcription factor jun-b. [swissprot;acc:p17275] Divided Low confidence 202.728 183.388 1.10546
66 fos-related antigen 1 (fra-1). [swissprot;acc:p15407] Subtracted 202.79 183.017 19.773
guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992] Divided High confidence 267.136 336.077 1.25807

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- Value Type describes how the microarray measurement was processed. Ranked indicates that we sorted all measurements and use the rank as red and green value. Measured is the normal measurement. Squared and Rooted are the square and square root respecitcely. This might be valueable to compensate for non linear light distributions.
- Network Comparison Type describes whether we divided the red and green types or whether we sutractcted them
- Interaction Map specifies whether we used only the hig hconfidence protein-protein interactions or also included the low confidence interactions.
- Filtered specifies whether we only included the high confidence microarry measurements or not.
- http://analysis.yellowcouch.org/